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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatatgtcaactactttgttttataacattgtagaattttacatattttgatctgttttaaaagtattgctctgcaaccctagtttttatcctat...

Basic information

species Glycine max
transcript GLYMA01G03260.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03260.3 (Glycine max), 5'ss of exon 4
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 5'ss of exon 4
GCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatatgtcaactactttgttttataacattgtagaattttacatattttgatctgttttaaaagtattgctctgcaaccctagtttttatcctat
||||| || ||||| ||||| || ||||||||| ||||||| || |||||||| ||||||||||||||||| |||||||| ||||| || ||||||||||||||     | | | |   | | |  |||     |      |   | | |      |  ||| ||   |  ||  ||||   |  |||            
GCTCCGTTTCTACTAGATGACCCAAATGTTGGAATGCTATTTCCAGCTGATGCTATTGCAAGAGCTAAACATTATCTTTCCTTGACTTCAGGCGGTTTAGgtatgaccttatgagcccatctataatatgtagattagtgttgacaaacagaacagttagttatatt-gcctttttctgtttcaatag------------

upper sequence: GLYMA01G03260.3 (Glycine max), 5'ss of exon 4
lower sequence: AT1G70580.2 (Arabidopsis thaliana), 5'ss of exon 4
GCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtat-tcatatgtcaactactttgttttataacattgtagaattttacatattttgatctgttttaaaagtattgctctgcaaccctagtttttatcctat
|| ||||| ||  | |||||||| ||||||||  || ||||||| || ||||| |||||||||||||| || |||||||| ||||| || || ||| | ||||| || | | | |   |       | | | ||| ||  |  ||  | ||    | | |||   || |  ||     |     | |   ||||| ||   
GCACCATTTCTGTTAGATGATCCAAATGTTGGTATGATATTCCCAGCAGATGCTATTGCAAGAGCTAAGCATTATCTTTCCTTGACTTCTGGTGGTCTTGgtatgtcttttattagagaac-----tcagatcatggttaatattggctta----ggtttgtacaaataacatgaaagtttttgctttacttttaaccag-
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19053398|gb|BM732065.1|BM732065
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|120529201|gb|EH257335.1|EH257335
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|14205452|gb|BG839130.1|BG839130
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|15285990|gb|BI469890.1|BI469890
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GTGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAATGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|7283746|gb|AW596349.1|AW596349
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|21887563|gb|BQ740776.1|BQ740776
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|23052838|gb|BU577329.1|BU577329
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGTGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|13481869|gb|BG511212.1|BG511212
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|23056339|gb|BU577717.1|BU577717
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|13480374|gb|BG509717.1|BG509717
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|298167407|gb|HO012670.1|HO012670
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGAC
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGAC
EST: gi|120491572|gb|EH219739.1|EH219739
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|20498442|gb|BQ273372.1|BQ273372
EST:     GCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: GCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|14205590|gb|BG839268.1|BG839268
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|15285988|gb|BI469879.1|BI469879
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
EST: gi|10847451|gb|BF070138.1|BF070138
EST:     TGCAATTGCAAGAGCTAAACACTATCTNTCATTGACCTCGGGCGGGTTAC                         GCGCTTATAGTGACTCCCGCCGCCTTCCA
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCA
EST: gi|213588415|gb|DB959735.1|DB959735
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAG                         GCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatat ... ggtgatgcagGCGCTTATAGTGACTCCCGCGGCCTTCCAGGAGTGAGGAAGGAAGTGGCTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCCATTCCTACTTGATGATCCTAATGTTGGACTGCTATTCCCTGCTGATGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGCGGTTTAGgtattcatatgtcaactactttgttttataacattgtagaattttacatattttgatctgttttaaaagtattgctctgcaaccctagtttttatcctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT